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1 : overbeek 1.6 # -*- perl -*-
2 : gdpusch 1.8 ########################################################################
3 : olson 1.7 # Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 :     #
8 :     # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 :     # Public License.
11 :     #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 : gdpusch 1.8 ########################################################################
18 : olson 1.7
19 : overbeek 1.2
20 : overbeek 1.1 use FIG;
21 : gdpusch 1.8 use FIGV;
22 : overbeek 1.1 my $fig = new FIG;
23 :    
24 : gdpusch 1.8 $usage = "usage: predict_starts [-orgdir=OrgDir] Objects ClearCalls ProposedCorrections";
25 :    
26 :     $orgdir_flag = "";
27 :     if ($ARGV[0] =~ /-orgdir=(\S+)/) {
28 :     $fig = new FIGV($1);
29 :     $orgdir_flag = $ARGV[0];
30 :     shift @ARGV;
31 :     }
32 : overbeek 1.1
33 :     (
34 :     ($objects = shift @ARGV) &&
35 :     ($clear_calls = shift @ARGV) &&
36 :     ($proposed = shift @ARGV)
37 :     )
38 :     || die $usage;
39 :    
40 : overbeek 1.5 &FIG::run("make_calls_for_start_predictions < $objects > $FIG_Config::temp/with.calls.$$");
41 :     &FIG::run("order_corrections_for_start_predictions < $FIG_Config::temp/with.calls.$$ 2> $FIG_Config::temp/clear$$ > $FIG_Config::temp/proposed$$");
42 :     system "cat $FIG_Config::temp/clear$$ >> $clear_calls";
43 :     system "cat $FIG_Config::temp/proposed$$ >> $proposed";
44 :     system "cat $FIG_Config::temp/with.calls.$$";
45 :     unlink("$FIG_Config::temp/with.calls.$$","$FIG_Config::temp/clear$$","$FIG_Config::temp/proposed$$");
46 : overbeek 1.2
47 :    

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